autosolvate.clustergen.startclustergen
- autosolvate.clustergen.startclustergen(argumentList)[source]
Wrap function that parses command line options for autosolvate clustergen, extracts microsolvated clusters from trajectory,
- Parameters:
argumentList (list) – The list contains the command line options to specify input trajectory, microsolvated cluster size, and other options related to microsolvated cluster extraction.
- Command line option definitions:
- -f, --filename
name of the .prmtop file
- -t, --trajname
name of .netcdf trajectory to extract the microsolvate clusters from
- -a, --startframe
first frame at which to start extracting from the trajectory the microsolvated clusters
- -i, --interval
interval in frames at which to extract microsolvated clusters from the trajectory
- -s, --size
solvent shell size for microsolvated clusters in Angstrom, upper limit for minimum solute-solvent distance
- -p, --spherical
switches from default aspherical solvent shell to spherical solvent shell, solvent shell size is now measured from center of mass, no argument required
- -r, --srunuse
option to run inside a slurm job, no argument required
- -h, --help
short usage description, no argument required
- Returns:
Generates the
`.xyzfile containing the microsolvated cluster- Return type:
None